ME3: Meet The Commander
by Mystical Ninja Unicorns
Summary: The series continues! In this one, I will bring back Rogue (my mass effect character) and romance her ;) Also rekindle the kaidan/shepard romance and resolve the Rahna issue, also i will make it so Kai Leng and Shepard use to know each other on the street, making the conflict sweeter. If I forgot anything else, it's probly in the intro. Read, review, and all that...
1. Chapter 1

_Alright! This is the ME3: Meet The Commander fan fic! I will be bringing back Rogue (my fictional character from ME2) and romancing her with James ^_^ Also I will be rekindling le Shepard and Kaidan romance also resolve the issues of Rahna from ME2, bring in a new thing for Shepard's stress and focus on how she handles it. Also since Kai Lang lived on Earth, then he will know Shepard on a personal level, making the conflict all the much sweeter. Oh and let's not forget a new ending to the game because I fucking hate the ALL endings of the game (makes me wanna rip my skin off and cry…. Maybe become a nudist!). Anyway, reviews, ideas, and all that crap are nice and after this no more new stories til I finish up my old ones, so feel free to check them out ^_^._

**Epilogue: Meet Commander Shepard**

The most painful thing about Earth was that she could do nothing. Shepard wanted to scream, cry, and find Harbinger and try to blow him up. She knew from the files she read that he personally led the attack on Earth for revenge. She had to trust Anderson, but she wanted to be down there, so did everyone else but Anderson told her that he wouldn't forgive her if she came back to Earth without a giant ass fleet of all the species, that she couldn't come back even if she wanted to.

"You know this is bigger than you and me, we need the whole galaxy if we want to win this…" Anderson said, ending it with a sigh and looking at Shepard, his old friend, with pity. He could see she was taking everything hard, just by her stance. She looked tired and defeated, but she never said anything about the stress she had. He knew from Joker's reports that came along with her battle suit information that she wasn't doing well. And this was just the start.

Shepard looked away; her purple pony tail landed onto her shoulder with the motion and looked un-brushed. She gave up on wearing the uniform; she just wore skinny jeans with either a thick white tank top or soft black t-shirt tucked into her pants with her regular combat boots. Today she wore the tank top, revealing the tattooed sleeve on her arm and new one on her chest, it was a skull with the wings on her collar bone, coving over her snake tattoo. "Doesn't mean I have to like it…" She mumbled, crossing her arms and not meeting Anderson's eyes.

Anderson sighed once more. "Shepard… You need to take it easy…"

Shepard's face flashed something, disgust maybe… "Listen, Anderson…" She met his eyes and he saw the sadness inside them, like you would glimpse inside a door about to close. And once that door closed the emotion were gone. "I gotta go…" She clicked off the terminal and walked away.

"Five minutes to Tuchanka, Commander." Joker said. "And Shepard…" Another sigh, as if that's all anyone could do when they saw or talked to Shepard nowadays. "He cares about you… we all do."

Shepard paused, and once again emotions tore at her chest, digging deep into her heart and eating it up, she needed to start blocking this out if she wanted to win. "Get the team ready." Shepard simply said, once again hiding behind her stone walled face and continuing on.

XXX

Joker wanted to rip out his hair, maybe punch Shepard a couple of times in the face. She wasn't being horrible to Joker or anything, just she kept hiding. Joker once again pulled up her suit readings and read it. Her implants kept failing on her, her biotics were slowly weakening, she gave up sleeping and eating, only sitting down for minutes before she rushed off, causing her to be eating very little and not sleeping at all. She took care of herself enough to not be stinky or greasy but she would be constantly busy. Even EDI was less of a robot than Shepard, and that was saying something.

"I am reading that you are frustrated Joker… Would you like to talk about it?" EDI said looking over at him from her co-pilot seat.

He softened at this, and looked over at the video of Shepard fighting on Tuchanka. After muting his side of the com, he sighed. "It's about Shepard." He said, looking over. "She's killing herself with all this stress, and she knows this, yet she doesn't talk about it. Not mentioning the fact that she closed up all her emotions and won't let anyone through."

"She did grow up on the streets." EDI said, looking at Joker unblinkingly.

"Yah, and…." Joker raised an eyebrow.

"She is using the same way of coping now as she did when on the streets… and on Torfan, maybe she needs the right person to reach out, for example when Anderson found her and rescued her, she stopped 'closing up her emotion' and joined the military. So until that certain person gets through, you must only support her and try to lessen the burden."

"Great…" Joker said, "You know you should be the ship's therapist." Joker said smiling.

EDI smiled back in her robotic way before going back to her work. And Joker once more sighed, becoming a habit of his whenever her though of Shepard, and he wasn't the only one.

XXX

"No!" Shepard's shout was rimmed with pain and love as she shot at the robot, one of the last things he heard before he lost consciousness. The first time he awoke it was blurry but he could see Shepard hadn't even left her armor yet, just sat there, looking at him with those sad green eyes. She held his hand, he could tell and suddenly his chest burned with love for her. As much as she denied it on Mars, she still loved him with all of her being. The second time he awoke, he could hear Shepard voice for just a second. "I need you…" She whispered in pain and then gave his arm a reassuring squeeze. That seemed to pull his eyelids up enough to watch her leave, and he couldn't help but smile, too bad he couldn't call her back, his voice stolen and frozen in his throat and then it just went black as the door closed behind her.

When Kaidan awoke, the white walls and light was a little too much. He heard sobbing… Shepard… no, Shepard doesn't cry, no matter what she doesn't cry… then it must be…

Kaidan opened his eyes to see Rahna looking at him. Suddenly she stopped and looked at him. "Kaidan…" She whispered.

"Rahna." He said, his voice scratchy. He cleared his throat. "What are you doing here?"

She raised her eyebrows and her mouth twitched. "You got hurt…" She whispered.

"Oh…" Kaidan whispered back, suddenly feeling stupid. "How are you feeling?" He asked.

"A bit tired… I was here all night…" Rahna said, wiping her tears away. Kaidan reached over and squeezed her hand gently. They weren't technically dating, but they still cared for each other.

"It's good of you to come here…" Kaidan said smiling encouraging at her.

"I was worried…" she said quietly.

"I'm fine, I just took a blow to the head." He said. That's when he noticed a flicker in her eyes. She seemed to unsure of something. "What…?" He asked, leaning a little towards her.

"Your commander… She care for you… doesn't she?" Rahna asked.

"Well I was under her command." He said.

"No… more than that…" Rahna said, making a burning sensation in his chest.

"Rahna… it's-"

The door suddenly opened to reveal his doctors. Kaidan sighed. "We'll talk about this later."

Rahna nodded and stiffly stood up.

XXX

The first time the black veins appeared, it was on Shepard's left arm. It started at her wrist then appeared on her bicep, craggily lines that climbed her arm, disappearing under thick skin then glowing through thin skin. They were veins the color of black and then they started appearing on her legs as well. Shepard asked about them, pointing them out after asking it be kept secret.

Chakwas gasped then grabbed her arm gently and took a closer look. "It's your implants…" She said. "Their starting to fail and so now they're slowly breaking apart and releasing chemicals from your increased blood pressure. Shepard… it may take a long time but if it reaches your heart... or your brain…. It may kill you after a while of it contaminating your organs."

"How can we fix it…?" Shepard asked.

"Without almost a year of rest and some surgery afterwards… nothing."

Shepard nodded. "Then we'll win this war before I die." Then she simply turned on her heel and left. But before she left the medical bay, she whispered, "Don't tell anyone… especially Anderson." Then she was gone, leaving the drowning sense of pleading for help.


	2. Chapter 2

**Ch1. Damsel in Distress**

_Back on Earth, just before Reaper attack…_

When the Reapers were about to attack, she could have warned Shepard. She was getting readings of something moving in from dark space, ready to warn Shepard, when the door opened and three menacing batarians walked through.

She leaned back in her spinning chair and looked as menacing as she could, and she did it quite well, because she could sense them falter for a second.

"You work for Cerberus?" She asked, standing up casually, as if they were simple cleaning men for her apartment.

"You already know the answer… That bounty they put on you is too great to pass up." The on in the front, obliviously their leader, said. He grabbed his gun and held it tight.

Rogue went on one knee, pretending to tie her high top black converse sneaker but really her fingers her pressing a small built in button that would open the window behind her as if a brush of wind did it and open up a small compartment that held two pistols below the window seal. Just as her finger was about to graze the button, when a pistol was cocked and she could feel the hole it was burning into her head. "Get up." The leader simply said.

Rogue held up her hands and stood up. There went plan A, Rogue thought, throwing a cocky smile at him. "Did I ever tell you I had a thing for batarians?" She asked.

"Oh really?" The leader asked, throwing up an eyebrow, it wasn't like he was interested in her, just the continuation of this statement.

"Yah, they're really fun to shoot in the eye balls and kill…" Rogue said shrugging. "Just an obsession really..."

The leader got close, filling in her vision with his face and putting his pistol to her neck. Before he could even snarl, she disarmed him with a simple punch to the wrist, then grabbing that same wrist, twisting it behind his back, catching the pistol in mid-air, and dislocating his shoulder, letting him drop to the ground, do a fancy back flip while shooting at the two other batarians, and breaking the window with her body. She clenched at the feeling of glass shards tearing her flesh but focused on landing. She was only falling from three stories into water.

She relaxed her body, and prepared herself for the crash. Once she hit the water, her breathe was stolen and water filled her nose for a moment. She lost the gun, and while cursing herself, swam to the surface and quickly to shore, her muscles from a life of crime pushing her through the water in ease. She ran by the building, pressing another hidden button that uploaded all the info on her data pads and computers to a simple implant that stored information in her head, and if the right password is spoken it would show up behind her eyes as if she was an AI. Then after a seamless second of easy upload, the apartment and all the computers would explode, destroying all evidence.

She then quickly grabbed the knife from the back of her pants and sprinted. She had her motorcycle for emergences in an abandon storage garage, all she had to do was get there, and across two streets. She knew she was getting reckless with her hacking, allowing Cerberus to get her location. Stupid, stupid, _stupid_! Rogue cursed as she ran down the street, her wet clothes hugging her body and chilling her bones as she passed surprised civilians, looking between her, the three wounded batarians, and the burning apartment. She lived near a lake; a place where you could touch the grass for it wasn't so high like the city across from the big lake. As Rogue went to cross the street, she was shot twice in the shoulder. She stumbled forward and tripped into the street, a car hitting her and catching her unaware. It stopped but not before making her roll over the car and hit the ground hard. She grunted, her ribs either broken or cracked, that and much worse. Thankfully, one of Rogue's implants instantly dulled pain after a certain amount is given to her, just in case she ever had a bad day or was being tortured.

Speaking of a bad day… Rogue thought as a pair of hands grabbed her ankle and pulled her away. She flipped over to see the two batarians with their one leader pointed a pistol in her face.

"They said you might try to escape." He said as one of the batarians injected a shot into her leg. She quickly noticed how fuzzy everything was getting and then they hauled her to her feet. "Nothing to see here." Was the last thing she heard before falling into the darkness.

XXX

When Rogue regained consciousness, she was half naked with nothing but her underwear and bra on and her arms were bonded in chains and pulled up. It hurt her right shoulder, most likely damaged when she hit the car. She began to rub her tongue against one of her molars. Looking for the small little switch on the side that if rubbed in a certain way, would call EDI for help, which Rogue implanted into the Normandy when no one was looking and when EDI was busy fighting off a bunch of small viruses that Rogue implanted for just a minute. It was something quiet that wouldn't be activated and release her signal when it was. Just as she felt the click, her cell door opened and revealed the leader of the batarians.

"Cerberus won't be here for a while, so they've asked me to try and get information…" He simply said, fisted his right hand.

"Try your best." Rogue said before punch to the gut stole her breathe.

"Now, tell us where your hidden implant is." He said, getting close and breathing on her menacingly.

"Which one?" She asked simply, another punch, to the face this time, she spat out blood and looked him in the eye. "When I get outta here, I'm going to fucking kill you… slowly." She whispered before another shot of pain.

XXX

Shepard was running on the treadmill tirelessly as she pushed herself further. She needed to be better if she wanted to defeat the Reapers, she told herself on day, so every morning she went to the gym and worked herself to near death. Then after a couple of minutes of rest, she would start again until her muscles were too weak to move. Then she would take a shower and get ready for the day. Sometimes she would do three to four missions in one day, siphoning out her companions and letting them rest as she endlessly pushed herself. EDI was what Shepard usually brought with her, since being a robot, EDI never got tired so most of the time even EDI wouldn't rest, not that it really mattered to her.

It didn't help with Anderson who was continuously bitching about rest and care, blah blah blah. Eventually Shepard just stopped talking to him, having Joker take the comm and talk to him instead. She knew it was disrespectful, but who cared, she needed to focus and Anderson wasn't really helping.

The black veins were slowly appearing on her belly, sprouting from her underwear like two hands on both her hip bones which stick out like she's a skeleton, and crawling up until her belly button where they faded away. Shepard was running out of time, she knew that, but she didn't care, she would fight or die, period.

Shepard stopped the treadmill to a walk and grabbed the sides, her lungs burned with the energy she just used and her back was soaked with sweat. She decided to cut the workout early that morning and go get something to eat, her hunger was killing her lately, but some days she just forgot about it and wouldn't eat until she sat down and realized the pain.

Shepard walked into the crew's quarters; none were up that early, maybe except Liara, who was working hard as well. Shepard opened the fridge of the crew's quarter; it was big and held a lot of fresh food, since Shepard wanted her crew to be well fed with fresh fruit and veggies. She grabbed a water bottle and a thing of grapes, throwing it on the counter while she chugged down the water. The deck was quiet and dark, the lights turned low until 0600 where some of the crew would wake up and then report to their post at 0800. Shepard turned on her electric cigarette, letting it fill with mist for a second as she put some grapes in a bowl, replaced the rest in the fridge and munched on each and every one, taking in the wonderful taste of fruit. When Shepard was a kid, she barely ate fruit, just manufactured products like cookies and granola bars. In fact the first time she ever ate until she was full was when she joined the military.

She also began to notice she was beginning to look like her old self from on the streets, extremely skinny with muscles packed in tight, pale skin, tired eyes. Not mentioning how everything felt like a dream. She felt numb all over, couldn't feel anything anymore. She didn't mind it, most likely cause from her stress, but it still felt strange, like a burned tongue, something you noticed and never forgot but could ignore most of the time.

"Been a long time since I saw you eat something while standing still." Joker's voice carried and tugged at the darkness.

Shepard smiled weakly. "You haven't been watching me eat again, have you Joker? Shall I remind you what happens when you stare at women?"

He chuckled then limped forward in his regular way, right up to the island counter that separated them and leaned against it with both palms on it. "I'll pass the lesson thanks." He smiled that smile that made his eyes cringle and look very warm.

"What are you doing up so early, Joker?" Shepard scrutinized him, squinted her eyes and took a drag of her cigarette, almost forgetting about it.

"I could say the same for you, you use to sleep like a bear in winter, but now you take… what? An hour nap?"

"That's about right, besides I have other things to worry about besides sleep." Shepard looked away for a moment and when she looked back, she noticed a flicker in Joker's eyes.

"You know, you are important to pretty much every one on this god damn ship?" He whispered.

"Not this again." Shepard moaned out as a whine.

"What? Do you not know when someone is trying to care about you?" Joker asked.

"Joker…" Shepard said quietly, the hum of the ship filled in the space. And then something shut inside of Shepard. "I can take care of myself, I know my limits."

"But you're Shepard right? Don't have my limits, because if you start to appear human then the universe might end right?" Joker asked mockingly.

"That's god damn right, Joker." Shepard said menacingly, stepping into better light.

That's when Joker saw it, the black vein on her arm. His eyes were glued to it, like it was a ghost waving at him, clear as day, not believing that he didn't notice it before. Shepard covered it with her hand and went back into the lower light. "What the hell is that?" He asked, obviously pissed that she hiding something from him.

"Nothing," Shepard said, grabbing her last grape, popping it in her mouth and then placing the bowl in the sink before turning over to Joker. She took a drag before turning to leave. "We've got better things to worry about Joker, don't you forget it."

XXX

"Shepard." EDI's voice called to Shepard from another nightmare. She dozed off at her desk again after her fight with Joker, and was working on technical ways to destroy the Reaper's desperately wishing Rogue was there.

Shepard jerked awake. "Yeah?" She asked a little drowsy and alarmed.

"There is a location that had been reported to me through an unknown way. It appears that Rogue installed something into my program that I had lately been ignoring. It is giving me her location along with an SOS. Shall we answer this?" EDI asked. "Note that the planet is under Reaper attack recently as well, so it may be hard to get to her."

"Send the coordinates to Joker, and get the team ready."

XXX

When Rogue awake, it was a good slap to the cheek. "I've woken up in better conditions." Rogue said again, earning another slap to the other cheek. The batarian then left her, obliviously not interesting in continuing her beating. She hadn't spilled a thing since she got there but her arms were killing her, and she felt like shit, covered in dirt, blood and sweat.

The batarians played poker until the leader got restless. "Where the hell are they?" He stood up, throwing his cards down and opened the latch that kept them all in this small confinement. He poked his head out, only to have it shot off, so he fell back with a thump, his head began bleeding on the floor.

Before anyone could utter a word, a cannibal reaper dropped in and shot the batarian closest to him. The other batarian shot at it, wounding it gravely, but another reaper dropped in and killed him. The two of them then began feasting on the bodies in front of her, not seeming to notice her.

Rogue barely breathed. They could easily rip her to sheds while she was still captive. The two cannibals looked up as a husk joined them, and fought for the three bodies. The husk killed one and then began to feed on the leader. The other cannibal then spotted Rogue and walked slowly up to her. He sniffed the air, unsure of what Rogue was. Rogue realized his confusion, she probly smelled partly an android, what with all the technology she put in her body.

He finally reached her, and the husk was right behind him. The cannibal watched as Rogue bent her legs so that her chain made her float in a way and folded her legs like she was a piece of paper. Then she quickly wrapped them around the cannibal neck and started choking him. He strangled and turned around, only making it worse for him as she sat on his shoulders and squeezed the hell out of his throat. Eventually he went limp as the husk watched curiously. Rogue then pushed the cannibal into the husk and made the husk fall then slide across the floor a good foot. He let out a battle cry and charged, and very fast.

Holding the chains above her, she pulled her body up at the last minute and was upside down and straight as a pencil as the husk rammed the wall behind her. Then she let herself go and used her body to slam into the husk with her shoulder. The husk hit his head and she felt his back snap in a couple of different places. Rogue pushed him harder into the wall, her shoulder forcing his neck at an awkward angle. Finally she snapped his neck and he fell to the ground. She then placed her foot on his neck and choked the air out of him so there was no chance he was alive.

Suddenly another cannibal dropped in. It fell, and then went limp and hit the floor. At first Rogue thought it would get up, as it raise its head, but then her favorite person in the whole world, pounced on him, her right booted foot landed right on his head and it exploded in a mess of gore. She then looked over at Rogue and smiled.

"Shepard." Rogue smiled. "About god damn time you got here."

Shepard smiled wearily back. "Why am I not surprised that you're tied up and half naked?"

Rogue laughed and watched as two other team members jumped in. Garrus and a human male that she didn't know. He had scars on his face and some sort of Mexican heritage.

"Damn…" He said smiling at her. "And who is this lovely Linda?"

Shepard rolled her eyes and broke the chain holding Rogue with her omni-tool. "Her name is Rogue." Shepard said, backing up and eyeing her.

"How's it been, Shep?" Rogue asked, popping her shoulder back in place and not even bothering to flinch.

"Oh, you know Reapers are finally here and we're all screwed." She said, shrugging her sholders.

"That explains why you look like shit." Rogue said then punching her in the shoulder. "But I take it your kicking their ass."

"More like their kicking ours." Shepard looked away as Rogue walked past her and opened a container with her things in it.

"Listen…" Rogue softened as she poured water on her, washing away most of the grime on her skin. "I was gonna warn you but… Cerberus caught up to me, and that's how I got in this mess."

"I was surprised that I didn't get your warning first, but now I know why." Shepard said, wrapping a blanket around Rogue. "Garrus grab her stuff," Shepard put her two fingers on her earpiece. "Cortes, come pick us up."

"Got it." Cortez answered as Shepard rubbed her temples.

"It's good to have you on the team again… unless you were planning to do something else…"

"Nah, man, I prefer to chill on your ship, nice and roomy, and I can walk around without worrying whether or not someone is going to stab me the gut." Rogue winked at Shepard. "Beside, you got the action going, I love it. Helps me do the good deeds of the day..." Her mouth twitched into a neat smile. "Always had trouble do those..."


End file.
